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PSA-Lab (psa-lab)

PSA-Lab

psa-lab

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Protein Structural Analysis & Design Laboratory at Michigan State University

Location:Michigan State University

Home Page:http://www.kuhnlab.bmb.msu.edu

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PSA-Lab's repositories

SimSite3D

The SimSite3D Software tools are designed to quickly search a database of three dimensional structures, in Protein Data Bank format, with protein-ligand binding sites to determine which binding sites in the database have steric and chemical similarities to the query binding site.

Language:GLSLLicense:GPL-2.0Stargazers:11Issues:4Issues:0

siteinterlock

A toolkit for predicting the binding mode of small molecules interacting with proteins based on interfacial rigidification, as assessed by graph theoretic constraint counting on the covalent and noncovalent bond network. Raschka et al. (2016) Proteins: Structure, Function, and Bioinformatics

Language:PythonLicense:GPL-3.0Stargazers:9Issues:2Issues:0

ProFlex

MSU ProFlex (formerly called FIRST) predicts the rigid and flexible regions in a protein structure, given a Protein Data Bank (PDB) file including hydrogen atoms.

Language:FortranLicense:GPL-2.0Stargazers:7Issues:2Issues:1

predicting-activity-by-machine-learning

Machine learning protocols for identifying biological activity determinants in the structural and chemical features of a set of small molecules that have been assayed. Useful for structure-activity relationship analysis of compounds identified by Screenlamp and other screening approaches. See Raschka et al. (2018) (ISBN 1-4939-7755-5)

Language:Jupyter NotebookLicense:Apache-2.0Stargazers:6Issues:2Issues:0

Consolv

A tool for predicting whether water molecules bound to the surface of a protein are likely to be conserved or displaced in other, independently-solved crystallographic structures of the same protein

Language:CLicense:NOASSERTIONStargazers:4Issues:2Issues:0

SLIDE

SLIDE is a computational screening and flexible docking tool designed to discover ligands with good steric and chemical complementarity to the known three-dimensional structure of a protein's binding site.

Language:CLicense:NOASSERTIONStargazers:4Issues:2Issues:0

Protein-Alignment-Tool

BRAT shows key residue (e.g., ligand-binding) correspondences between sequence-divergent homologs aligned by structural superposition. BAT displays residues and their numeric properties (from the B-value column) of PDB structures, given their structural superposition.

Language:PythonLicense:GPL-3.0Stargazers:2Issues:2Issues:0

protein-recognition-index

Calculates the Protein Recognition Index (PRI), measuring the similarity between intermolecular H-bonding features in a given protein-ligand complex and the H-bond trends observed in diverse protein-ligand complexes. Raschka, Wolf et al. (2018) JCAMD

Language:PythonLicense:Apache-2.0Stargazers:2Issues:2Issues:0

Sequery

Sequery is a tool to search the sequences of the protein structures in the Protein Data Bank (PDB) for a particular pattern of residues, which may include exact matches and acceptable substitutions based on a user-specified amino acid substitution matrix and/or a numerical threshold.

Language:AGS ScriptStargazers:2Issues:2Issues:0

Hbind

Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka, Wolf, et al. (2018) J. Computer-Aided Molec. Design

Language:CLicense:Apache-2.0Stargazers:1Issues:2Issues:0

screenlamp

screenlamp is a Python toolkit for hypothesis-driven virtual screening. Raschka, Scott, et al., (2018) JCAMD

Language:PythonLicense:Apache-2.0Stargazers:1Issues:2Issues:0

WatCH

WatCH is a tool for the calculation of conserved water sites in a series of related structures in Protein Data Bank files.

Language:CLicense:NOASSERTIONStargazers:1Issues:2Issues:0

HbindViz

Generates a script to visualize protein-ligand H-bonds from an Hbind interaction table (see separate Hbind module) for display by PyMOL. Raschka, Wolf et al. (2018) J. Computer-Aided Molec. Design

Language:PythonLicense:Apache-2.0Stargazers:0Issues:2Issues:0

SpeciFlex

A tool to generate contour for volumes sampled via MD trajectories as well as computing difference-volumes from two trajectory volumes

Language:CLicense:GPL-2.0Stargazers:0Issues:2Issues:0

SSA

SSA is a tool to assign the secondary structure of a peptide from its atomic coordinates in PDB format based on their superposition with sequences of ideal secondary structure

Language:CLicense:NOASSERTIONStargazers:0Issues:2Issues:0